Is there a way to automatically add faces in proper places to this mesh?
Use a boolean modifier




Add a Cube scaled to flat in the desired location without hole. You may not even need to be precise because your edges may be intended to be hidden in frame. Or use F as you mentioned above. Assume name window01.
Create a sphere named  Sphere01.  Sphere01 will be the hole cutter.
Add a boolean modifier [difference]  to window01.  Sphere01 is target of modifier .  
Position Sphere01 where the desired hole should be.  You may hide the sphere to view easily ,  or view in wireframe mode.  You can use multiple spheres or other deformations of the sphere.  You determine placement.
Press apply button for the boolean modifier.
Reshape hole produced by the boolean modifier on window01. You might enjoy proportional editing in edit mode for this.
Duplicate window01 to new locations or repeat process for each new window.